SMTL ID : 6dht.1

Bacteroides ovatus GH9 Bacova_02649

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

monomer

Ligands

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.1: 14 residues within 4Å: Chain A: D.168, A.169, G.170, N.178, Y.333, W.437, Y.544, E.548, V.549, A.550, N.552, W.553 Ligands: EDO.4, PEG.20 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.333, A:E.548 pi-Stacking: A:W.553

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 7 residues within 4Å: Chain A: D.335, H.337, A.338, D.340, E.341, G.376, N.377 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.335, A:H.337, A:D.340, A:E.341, A:G.376 CA.3: 6 residues within 4Å: Chain A: E.206, S.207, N.209, T.211, D.213, D.216 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.206, A:T.211, A:D.213, A:D.216, H2O.12

14 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 9 residues within 4Å: Chain A: G.331, E.332, Y.333, G.334, W.375, W.437, Y.544 Ligands: IMD.1, PEG.19 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.332, A:Y.333 Water bridges: A:G.334 EDO.5: 7 residues within 4Å: Chain A: G.170, D.171, F.245, F.248, H.497, R.499, Y.544 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.499, A:R.499 Water bridges: A:D.171, A:D.171 EDO.6: 5 residues within 4Å: Chain A: D.109, A.110, K.113, I.202, N.203 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.109, A:K.113 Water bridges: A:A.110 EDO.7: 7 residues within 4Å: Chain A: S.198, K.201, N.209, H.210, T.211, P.212, Y.285 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.209 Water bridges: A:D.213 EDO.8: 6 residues within 4Å: Chain A: Y.190, Q.191, L.194, R.280, L.281, Q.388 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.280 Water bridges: A:Q.388, A:Q.388 EDO.9: 7 residues within 4Å: Chain A: Y.350, F.351, G.354, R.391, E.392, L.393, D.397 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.350 EDO.10: 4 residues within 4Å: Chain A: E.356, R.359, E.360, I.363 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.359 EDO.11: 7 residues within 4Å: Chain A: W.386, L.387, R.398, A.401, D.402, K.405, Q.457 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.398, A:R.398, A:D.402, A:D.402 Water bridges: A:Q.457, A:Q.457, A:Q.457 EDO.12: 7 residues within 4Å: Chain A: A.366, P.367, Q.368, F.400, S.403, L.404, E.407 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.368 EDO.13: 6 residues within 4Å: Chain A: Y.455, D.461, L.464, T.465, Y.468 Ligands: EDO.14 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.465, A:T.465 Water bridges: A:Y.455, A:D.461 EDO.14: 7 residues within 4Å: Chain A: Y.26, N.28, Q.29, E.30, Y.468, A.568 Ligands: EDO.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.568 Water bridges: A:N.28, A:E.30 EDO.15: 5 residues within 4Å: Chain A: L.192, F.193, P.389, L.456, L.567 No protein-ligand interaction detected (PLIP) EDO.16: 4 residues within 4Å: Chain A: L.393, N.394, E.395, R.398 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.398 EDO.17: 4 residues within 4Å: Chain A: D.195, Y.196, R.199, A.566 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.199

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.18: 7 residues within 4Å: Chain A: A.372, Y.411, V.415, E.442, K.443, Q.447 Ligands: CL.21 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.447 Water bridges: A:V.415 PEG.19: 5 residues within 4Å: Chain A: W.437, N.519, Y.544, A.545 Ligands: EDO.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.519 Water bridges: A:W.437 PEG.20: 14 residues within 4Å: Chain A: Y.181, Y.333, P.373, G.374, W.375, F.436, W.437, G.438, A.441, E.442, N.446, N.552, W.553 Ligands: IMD.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:W.375, A:W.375, A:E.442, A:N.552, A:W.553 Water bridges: A:Y.181, A:N.552

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.21: 4 residues within 4Å: Chain A: T.371, A.372, Y.411 Ligands: PEG.18 Ligand excluded by PLIP CL.22: 5 residues within 4Å: Chain A: D.171, Y.172, N.173, F.245, E.246 Ligand excluded by PLIP

1 x MG: MAGNESIUM ION(Non-covalent)

MG.23: 3 residues within 4Å: Chain A: S.501, D.504, I.506 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.501, A:D.504, A:I.506, H2O.5, H2O.10, H2O.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Foley, M.H. et al., A Cell-Surface GH9 Endo-Glucanase Coordinates with Surface Glycan-Binding Proteins to Mediate Xyloglucan Uptake in the Gut Symbiont Bacteroides ovatus. J. Mol. Biol. (2019)

Release Date

2019-04-03

Peptides

Xyloglucan-specific endo-beta-1,4-glucanase BoGH9A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Xyloglucan-specific endo-beta-1,4-glucanase BoGH9A